4YGO

Dodecameric structure of spermidine N-acetyltransferase from Vibrio cholerae in intermediate state

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.01 M CaCl2, 0.1 M Tris HCl, 20% Methanol, 25 % MPD

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 155.118	α = 90
b = 135.793	β = 117.13
c = 72.848	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 225 mm CCD		2011-12-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-F	0.97872	APS	21-ID-F

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.5	30	100	0.065	25.4	3.8		46610			54.8

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.54	100		0.59	2	3.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3EG7	2.5	30	44197	2408	99.35	0.18368	0.18011	0.25274	RANDOM	61.62

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-3.99		-1.54	0.6		3.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.805
r_dihedral_angle_3_deg	18.511
r_dihedral_angle_4_deg	18.158
r_dihedral_angle_1_deg	7.202
r_long_range_B_refined	5.587
r_long_range_B_other	5.58
r_scangle_other	3.846
r_mcangle_it	3.069
r_mcangle_other	3.069
r_scbond_it	2.532
r_scbond_other	2.532
r_mcbond_it	1.979
r_mcbond_other	1.978
r_angle_refined_deg	1.762
r_angle_other_deg	1.052
r_chiral_restr	0.104
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8611
Nucleic Acid Atoms
Solvent Atoms	144
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
BLU-MAX	data collection
HKL-3000	data scaling
PHASER	phasing
Coot	model building
HKL-3000	phasing